When I export my Scrivener files into “.txt” or “.md” format, I obtain this ugly thing at the end :
As you can see, the “é” or “ù” or “à” characters are not recognised.
This happens when I import to from external .md or .txt however, I can obtain a clean scrivenir file if I select “UTF-8” encoding.
Would it be possible to make the choice “UTF-8” available for the whole “in” and “out” process ? I can’t choose “UTF 8” for export md, and I have to manually check “utf-8” for txt and md too.
Below is what the Mac v3 manual says about UTF-8. I suspect it’s true for the version you’re using as well.
[attachment=0]section 9.1 - file import.png[/attachment]
The encoding prompt is available when you export to MMD too. Make sure you reset your warnings (File > Options > Warnings), in case you have previously stored your preferred encoding.
It does not help at all. The manual could say whatever it wants, the fact is I have to manually verify every single file while working or I could find glyphes instead of accents. The fact is it does not happen if I chose “UTF8” manually. So… what your citation can do for me here ? 
Thank you, the window is here and I can choose. I will win a lot of time ! 
Is it possible to add a global option when choose an encoding once ?
When you select “Do not show this dialog again” your current selection will be saved for future use without a prompt. Having this available in the Options is also something we think about, but not in our priority list at the moment,